Bolsonaro has been arrested after authorities concluded he posed a concrete flight risk while under house arrest.
The former head of state was found guilty of orchestrating a armed takeover in the ninth month and sentenced more than 27 years in jail, but he remained under house arrest pending appeals.
Top Judicial Official Justice Moraes said the decision to arrest the 70-year-old politician was a precautionary step after recent developments emerged.
This included trying to remove his electronic bracelet and a invitation to a supporters' gathering that could enable a chance to flee".
In a document approving the custody, the judge said information from the centre monitoring Bolsonaro's house arrest suggested the ex-president's "intention to break the tracking monitor to secure accomplishment in his getaway".
This, it said, would be assisted by the chaos caused by the demonstration called by his son.
His offspring, Flávio Bolsonaro, who holds office as a congressional representative, called for a assembly of his backers near Bolsonaro's home to take place on the weekend.
His son wrote on social media on last Friday: Will you battle for your country, or watch it all from your smartphone there on your settee? I call on you to fight with us."
He said the vigil would be so backers could "pray for his health and for the restoration of democratic rule in our nation."
Part of Justice Moraes's decision was the possibility of Bolsonaro's transfer to diplomatic missions near the home, considering that the investigations revealed a history of organizing to request asylum through a embassy office", a declaration said.
The judicial paperwork underscores that the American diplomatic mission in the federal district, Brasilia, is located around 8 miles from his dwelling.
Bolsonaro's legal woes have drawn the ire of fellow right-wing populist US President Trump, leading him to implement a fifty percent tax on goods coming from Brazil.
The former president is being kept in a federal law enforcement building in Brasilia and will experience a imprisonment assessment on the following day.
It was only on the previous day that the his legal team asked the Supreme Court to authorize him to complete his entire prison term under house arrest, with electronic monitoring.
They also asked that Bolsonaro be allowed to depart his residence for healthcare, saying he demanded regular treatment for respiratory ailments and other illnesses.
Bolsonaro was convicted of heading a conspiracy aimed at retaining his authority after he was defeated in the 2022 election to his left-wing rival, Lula.
Top judicial officials said that he had knowledge of a plot which encompassed plans to assassinate the current president and his VP candidate, his vice-presidential candidate, and to imprison and murder Alexandre de Moraes - the Supreme Court justice who has been overseeing Bolsonaro's trial.
The conspiracy was stopped because it couldn't obtain the endorsement of the military leaders. His successor was sworn in without incident on the first day of 2023.
But a following week, on the eighth of January, thousands of Bolsonaro supporters invaded and destroyed official structures in the national capital, Brazil's capital.
The police intervened and around approximately 1,500 persons were arrested.
The judges found that the protesters had been incited by Bolsonaro whose scheme, they said, was for the country's army to intervene, bring back stability and bring him back to power.
At the moment, Bolsonaro's lawyers called the over 27-year sentence extremely harsh.
He was also prohibited from campaigning for office until the year 2060 - eight years after the completion of his term.
The ex-leader called the court case a "witch hunt and said it was intended to stop him competing in the 2026 presidential election.